It's been my experience that it's one of those things that you have to develop as you go for different species, and sometimes different situations. For me, I probably use a strip strike more than anything, then raise the rod to get the pressure on the fish. Took me a long time to get out of the habit of striking with the rod. I still do it with other tackle, and have even gotten away from the cross their eyes Bassmaster type hook sets with other tackle. Still, it's a hard habit to break & sometimes I still get carried away.
Most of the fishing I do is for bass, or Striped Bass & they tend to hit hard, so strip strikes work well, as many times they'll hook themselves. When I fish for panfish, I still just lift the rod, even though my intention is to use a strip strike. They often hook themselves too.
My biggest challenge is with topwater flies, since seeing the strike and reacting is natural, and striking with the rod is natural. Still, I know to be patient, not over react & strip strike when I feel the pull. Just doesn't always work as I intend!